Taxonomy as a Rigorous Science

[Akri]

Dinwar, I didn't say discard it, it's all you have. I just think relying on morphology alone when you don't have a high enough percentage in the fossil record to represent the population isn't going to give you an accurate idea of who and where we came from if DNA is out of the question.

Yes, we know what you think. The question is do you have data to support your opinions? You keep saying that the low number of fossils is a problem. We're waiting for you to actually demonstrate that this is so.

Additionally, you're saying that paleontological methods are unreliable. If you're not also saying those methods should be discarded then you're being contradictory. If the methods don't work then why keep them?

DNA technology improves exponentially every year. Who is to say once we unravel it all that it won't be more informative piecing the story together from living taxa, much like you do already with morphology, but less subjective IMO.

So you're criticizing paleontology for being less reliable than a hypothetical future version of genetic research? Should we take this to mean you can't present any evidence of paleontology being less reliable than currently-existing genetic research?

 

[Dinwar]

I just think relying on morphology alone when you don't have a high enough percentage in the fossil record to represent the population isn't going to give you an accurate idea of who and where we came from if DNA is out of the question.

And you maintain this stance despite the fact that I've demonstrated that where DNA and morphological evidence are both present, and used independently, they provide exactly the same results.

Jodie, at this point you are arguing nothing but pure intrincisism. You are saying that in some magical and unspecified way, DNA-based phylogenies are better than morphologically-generated phylogenies despite the fact that the trees are identical. And yes, that IS what you are saying--because in the examples givin in this thread, the trees ARE identical and you STILL reject the morphological data.

Secondly, you drastically underestimate the number of fossils we have. Hominids have a surprisingly good fossil record, but they're still terrestrial vertebrates. I've personally handled over 50,000 brachiopod fossils in my lifetime so far. I know that it's at minimum 50,000 because I was helping catalogue them for a small fossil collection at a minor state university while I was an undergrad. 20,000 came from the same species. When you get to marine invertebrates with shells, our fossil record is good enough to show speciation events (not in as much detail as hominid fossils, but you have to understand that we're looking at speciation events in the Paleozoic here; having ANYTHING from such a short-lived event is impressive). And even those fossil records pale in comparison with forams, diatoms, radiolarians, and the like.

Even if we accepted the insane and demonstrably untrue idea that we must ignore morphology as a means of constructing a phylogeny in vertebrates(and "not having an accurate idea of who and where we came from" is merely a verbose way of saying that we are incapable of constructing an accurate phylogeny), we still have ample reason to utilize those techniques on INvertebrates. And if you don't see how that informs us about where we came from, you have no business discussing evolution.

DNA technology improves exponentially every year.

So does more traditional paleontology. There are thousands of us paleo folks; we don't just sit around. You are once again revealing your ignorance about a field you've chosen to attack.

Who is to say once we unravel it all that it won't be more informative piecing the story together from living taxa...?

Basic logic and reasoning. "Extinct" means the creature no longer exists. That means there is NO way to get ANY genetic information outside of the most recent fossils, meaning the last few tens of thousands of years--Holocene to Late Pleistocene. For the USA, it's the Rancholabrean to perhaps the middle Irvingtonian. DNA simply doesn't survive past that point, and without a living specimen that means that the genetic information is irrevocably gone. Period.

Your options for genetic analysis for anything older than the Irvingtonian are pure guesswork or a time machine. And you want us to pretend that THAT is more objective based on nothing other than "Someone on the internet who can't even be bothered to learn the names of the sciences she's attacking says so".

Have you published your ideas in that journal yet? Have you even bothered to draft them into something coherent enough to count as the start of a paper?

 

[Jodie]

And you maintain this stance despite the fact that I've demonstrated that where DNA and morphological evidence are both present, and used independently, they provide exactly the same results.

Not always.

Jodie, at this point you are arguing nothing but pure intrincisism. You are saying that in some magical and unspecified way, DNA-based phylogenies are better than morphologically-generated phylogenies despite the fact that the trees are identical. And yes, that IS what you are saying--because in the examples givin in this thread, the trees ARE identical and you STILL reject the morphological data.

Obviously when DNA is missing they aren't identical. Did I not just link you the article where they are considering doing away with all of the Homo Erectus subspecies based on the skull they found recently? The only reason they would have developed so many subspecies of Homo Erectusis is if they didn't know what the variation within the species was to begin with.

Secondly, you drastically underestimate the number of fossils we have. Hominids have a surprisingly good fossil record, but they're still terrestrial vertebrates. I've personally handled over 50,000 brachiopod fossils in my lifetime so far. I know that it's at minimum 50,000 because I was helping catalogue them for a small fossil collection at a minor state university while I was an undergrad. 20,000 came from the same species. When you get to marine invertebrates with shells, our fossil record is good enough to show speciation events (not in as much detail as hominid fossils, but you have to understand that we're looking at speciation events in the Paleozoic here; having ANYTHING from such a short-lived event is impressive). And even those fossil records pale in comparison with forams, diatoms, radiolarians, and the like.

You might have 50,000 fossils of some kind of marine life but hominid fossils aren't so plentiful, which is what I'm talking about.

Even if we accepted the insane and demonstrably untrue idea that we must ignore morphology as a means of constructing a phylogeny in vertebrates(and "not having an accurate idea of who and where we came from" is merely a verbose way of saying that we are incapable of constructing an accurate phylogeny), we still have ample reason to utilize those techniques on INvertebrates. And if you don't see how that informs us about where we came from, you have no business discussing evolution.

No one suggested ignoring morphology except you, I simply stated I thought it was subjective. I provided the statistical demonstration based on the Neanderthal population as to how many Neanderthal fossils would be needed to truly represent the population. As you said, there are ways around this, but since the hominid record is continually revised I think I have a point about the limitations of using morphology alone.

So does more traditional paleontology. There are thousands of us paleo folks; we don't just sit around. You are once again revealing your ignorance about a field you've chosen to attack.

No, I think the paleontologists have to have a working knowledge of several fields to be able to function.

Basic logic and reasoning. "Extinct" means the creature no longer exists. That means there is NO way to get ANY genetic information outside of the most recent fossils, meaning the last few tens of thousands of years--Holocene to Late Pleistocene. For the USA, it's the Rancholabrean to perhaps the middle Irvingtonian. DNA simply doesn't survive past that point, and without a living specimen that means that the genetic information is irrevocably gone. Period.

No it doesn't, but we are a long way from recognizing what every SNP's is responsible for what, if anything at all, or how an orchestra of genes might express a certain way. We are just finishing mapping and developing data bases. However, one day we will be there, and with that knowledge you can look into the living taxa and pull out what was ancient and where it derived from. I don't think I'm alone in that thought:

http://www.theguardian.com/science/2011/apr/25/mitochondrial-dna-human-evolution

http://www.actionbioscience.org/evolution/ingman.html

Your options for genetic analysis for anything older than the Irvingtonian are pure guesswork or a time machine. And you want us to pretend that THAT is more objective based on nothing other than "Someone on the internet who can't even be bothered to learn the names of the sciences she's attacking says so".

Have you published your ideas in that journal yet? Have you even bothered to draft them into something coherent enough to count as the start of a paper?

Why would I write a paper on paleontology? I wouldn't, but you could, it's your field, I could ask you the same question.

 

[Akri]

Not always.

Evidence?

No one suggested ignoring morphology except you, I simply stated I thought it was subjective.

The thing is, if morphology is unreliable (which is what you're arguing) then why the hell shouldn't we ignore it?

Why would I write a paper on paleontology? I wouldn't, but you could, it's your field, I could ask you the same question.

Why wouldn't you? You're criticizing the field. You think you've spotted problems with it that the experts don't see. Why not write a paper on the topic?

As for asking him the same question, why on earth would he write a paper about flaws that he doesn't believe exist?

 

[Dinwar]

Not always.

I have spent weeks inviting you to substantiate this claim, and you refuse to.

The only conclusion I can draw is that you are incapable of doing so. You think you're really good at the large-scale issues, but your utter incompetence with the nitty-gritty of the fields you attack betrays you. You CANNOT understand the large-scale issues in any field without understanding the details; if you try, you fall into the types of traps you've found yourself in, accepting demonstrably wrong arguments because they sound good without understanding the trivial flaws that destroy the arguments.

Did I not just link you the article where they are considering doing away with all of the Homo Erectus subspecies based on the skull they found recently?

You linked to an article saying that some people argued they should. I provided sound paleontological arguments as to why they shouldn't. You don't get to ignore things simply because you refuse to educate yourself to the point where you understand their implications. And I DO get to argue that they don't necessarily need to be united, because I've presented coherent arguments backed by biological evidence. That's one of the joys of being involved in a field of science: I get to tell people they're wrong, even the experts.

The only reason they would have developed so many subspecies of Homo Erectusis is if they didn't know what the variation within the species was to begin with.

Which is not the same as saying that the original hypothesis was subjective. You also do not get to re-define all errors to be the specific error you wish them to be. I've always admitted that paleontology revises its hypotheses to match the data--that's called empiricism, not subjectivity, and is a requirement for a field to be considered a science. You're the only person I've met outside of hard-core Creationists that uses the argument "Scieince changes its mind, therefore it doesn't work".

You might have 50,000 fossils of some kind of marine life but hominid fossils aren't so plentiful, which is what I'm talking about.

Translation: you don't care about evidence. You're so narrowly focused on a single taxon that you are unwilling to examine the rest of the field, despite (or because of, perhaps) the fact that as soon as you do your arguments fall apart.

No one suggested ignoring morphology except you, I simply stated I thought it was subjective.

The fact that you don't see the equivalence in these statements demonstrates how little you know about the fields you are attacking. The fact that you ignore the fact that morphology demonstrably produces the same phylogenies as genetics means you're a crackpot (I honestly don't know what else to call someone who so fervently ignores data).

You have two options, Jodie: either morphology is not subjective, or genetics is. Since they produce essentially identical results, there is no way for one to be subjective and the other to not be.

Oh, and just to bring this point up again, since you still persist in ignoring it: the selection of genetic features to compare between species is every bit as arbitrary as the selection of morphological features. Which is to say, it's not--there are ways to test if the traits you've selected are worth including or not--but my point is, the process for selecting traits to compare is identical regardless of what class of traits you're comparing. So your options are limited to either both morphology and genetics being subjective, or neither being subjective. Since you have yet to offer any substantiating evidence supporting the notion that morphological methods are subjective (again, simply showing that later data can disprove a working hypothesis IS NOT the same as showing that the process was subjective--the exact same thing happens with genetics, all the time, you just don't hear about it because of your absurd and wholly irrational focus on hominids), we can dismiss the idea of either being subjective.

No, I think the paleontologists have to have a working knowledge of several fields to be able to function.

This has nothing to do with my response, and if you knew anything about paleontology you'd know that only polymaths have even the slightest chance at it. At minimum we need to know biology and geology--in fact, my undergrad work was essentially a dual major in bio and geo. But that's just the tip of the iceburg, believe me.

No it doesn't, but we are a long way from recognizing what every SNP's is responsible for what, if anything at all, or how an orchestra of genes might express a certain way.

Again, you've dishonestly ignored my point (dishonest because I flat-out stated it, repeatedly). My point is that for all but the tiniest sliver of the most recent organisms we do not and cannot have genetic data. There's literally NOTHING to work with in terms of genetics. ANYTHING past the Middle Irvingtonian REQUIRES us to use morphology. Your methodology is completely, demonstrably, and irrevocably unworkable in deep time. Which makes it useless for the very fields to which you want to apply it.

What you're doing is the equivalent of asking a mechanic to fix a horse. It makes no bloody sense.

Why would I write a paper on paleontology?

Because you came into this forum and started attacking the entire field. If you're not a coward, you will present these arguments in the proper forum. Otherwise you're essentially saying that your arguments aren't good enough to withstand the analysis of those you are attacking. They're not--I've presented a number of critical flaws in them, and believe me, other paleontologists WILL find more--but the fact that you cling to these ideas despite the evidence suggests that you're unwilling to accept that. Fine; stand by your convictions. Present your arguments to those you believe are acting in error. Or refuse, admitting that your arguments are invalid.

...it's your field, I could ask you the same question.

This phrase makes no sense. Either you're asking why I don't publish in my field, which is demonstrably wrong--I publish rather frequently, and I've presented talks at two international conferences (okay, one was a conference between the USA and Canada, but it still counts)--or you're asking why I don't publish YOUR ideas--which is insane, because I think your ideas are based off of willful ignorance and an unhealthy focus on a single taxa, and they completely fall apart once you actually learn anything about the fields involved. Either way, the question is nonsense. And I'm certainly not going to waste my time publishing a rebuttal to an argument who's proponant can't even muster up the courage to present the argument; there's no value in it, as nothing I've said would be news to any paleontologist worth their rock hammer.

 

[Kotatsu]

No one suggested ignoring morphology except you, I simply stated I thought it was subjective.

Maybe this has been covered before, but in what way is genetic data less subjective than morphological data?

People who do genetic phylogenies will still need to chose the genes they will sequence (1), and they will need to chose which gene trees to publish, or at least which gene trees to put most emphasis on if the different genes show different things. There are thousands of published phylogenies out there where the authors clearly want a certain scenario to be true, and therefore put more emphasis on trees that are concordant with that scenario, and relegate mismatching trees to "Electronic material" or simply do not publish it.

There's also (at least in the past, I haven't done any sequencing for a few years) the issue of reading chromatographs and trying to establish in tricky areas which of two equally high peaks in a certain position is the accurate one, or if both are accurate, and if so what to do with them: prune? use one of those hybrid letters? decide on one letter?

What method do you use to align your data set? What do you do with hypervariable sections? Do you include or exclude the primer regions from the alignment? If you use multiple analysis methods (parsimony, bayesian, likelihood, and so on) what parametres do you use? Do you treat trees from all three analyses equally? What if they don't say the same thing? Which analyses will you put in "Electronic supplements" or just not publish? If you get an unexpected or very unlikely placement of a taxon, do you just cut it out, resequence it (from the same or a different specimen?), or see this as a result in itself? Do you try to ascertain that the specimen is actually the taxon you thought it was, or do you just assume that it is (2)? How do you chose an outgroup? How do you select which taxa should be included in the ingroup? Do you change these two to get the results you want? (3)

These are just some of the long list of reasons why a genetic phylogeny is about as subjective as one based on morphology. What can generally be said is that someone who takes the time to construct a morphological data set and turn that into a phylogeny probably has a more intimate knowledge of the group in question that someone who only see the taxa as small samples in tubes from which they will extract DNA.

When I worked with bird phylogenies as an undergraduate-equivalent, I was given bags with feathers in them and extracted DNA from them. I had no idea whether the identification of the taxa was correct, and the feathers (from warblers, finches, and sparrows, mainly) were too uniform to be able to tell anything useful from studying the feathers. Now that I also do morphology, and am lucky enough to be in a lab that sees the worth of combining morphology and genetics in reconstructing phylogenies, I understand the group I'm working with (feather lice) infinitely better than I did when I worked with birds.

Case in point: a friend of mine was working with the systematics of a minor phylum of animals, on which there are about three living experts. His supervisor didn't know anything about the group, but had still somehow managed to get funding for this PhD project, so they looked up these few experts, and found that only one was in Europe, where my friend was also living. It would make more sense to fly down to Italy from Sweden every now and then, than to fly to (I think) South America and Australia where the only other two experts worked.

So my friend collected a lot of material, sequenced this, and brought it to Italy, where he was going to collaborate with the expert and make the first phylogeny of the group to incorporate all described families. However, when the results came back from the (I think) Bayesian analysis, there were lots of species that came out in the "wrong" family, and the trees made little sense when compared to the scenario of the evolution of this group that the Italian professor had already proposed (presumably based on morphology or on smaller data sets; I don't know). The Italian therefore started deleting taxa from the data set that he thought were placed in the wrong part of the tree,until he got the scenario he wanted. My friend tried to stop him, but the Italian simply pointed out that he was the professor, my friend was the PhD student, this was the professor's lab, and therefore they were going to do things his way. Luckily, my friend had saved all the data.

This story is meant to show one thing: it doesn't matter what data you have, because it's going to be filtered through a human at some point, and then all pretense of absolute objectivity vanishes immediately. There is no actual qualitative difference between the objectivity of genetic characters and morphological characters; there is only a difference in how they are treated.

The statement that genetic data is less subjective than morphological data is a myth, perpetuated mainly by people who have a vested interest in getting their publications into higher-ranking journals or getting more funding.

---
(1) Unless, of course, this is chosen for them. There are only a handful of primer-pairs that have been used for louse phylogenies, for instance, because early on there were only a few that could be made to work, and this has sort of channeled new sequencing into certain gene regions, as people want to compare new data with old data, or incorporate older sequences in new data sets. This is true for most unpopular groups of organisms (i.e. everything except birds and wasps...).
(2) Many phylogeneticists DO NOT KNOW the species they are working with intimately enough to be able to tell closely related species apart. They have no interest in taxonomy, and do not even try to make sure that the name they are using is actually the correct one.
(3) Of course, many of these issues exist with morphological data as well.

 

[Akri]

Snip

That is an excellent post. Way to keep the 'E' in 'JREF'.

 

[Dinwar]

Well said, Kotatsu!

(2) Many phylogeneticists DO NOT KNOW the species they are working with intimately enough to be able to tell closely related species apart. They have no interest in taxonomy, and do not even try to make sure that the name they are using is actually the correct one.

That's depressing. I know that in paleontology there's still a big enough push for morphology that even those who use genetics need to have a basic understanding of the taxa they're examining, but that's as much due to inertia as anything else (for hundreds of years we had nothing BUT morphology to work with, so paleontology focuses on morphology). It's rather frightening that this isn't the case for the squishier fields of biology.

(3) Of course, many of these issues exist with morphological data as well.

On page 28 of my copy of Valentine's "On The Origin of Phyla", the page where he discusses phylogenies and constructing them, I drew in what the tree he used would look like if it were run using ACCTRAN instead of LACTRAN, two different settings in PAST. The differences weren't huge, but there were definitely character changes moved around!

The big issue with morphology, particularly with ancient organisms, is determining whether or not your characters are subjet to evolution. Surprisingly, not all morphological traits are. Some traits are simply due to the structural necessities of other traits--Gould had a name for them, but it always eludes me. Other traits are due to environmental factors--for example, humans that have better nutrition grow taller, regardless of genetics. And if you really want to mess with your head, try to figure out how chronospecies fit into this. Bison antiquis essentially turned into modern bison (creatively enough, B. bison) wholesale. How do you represent THAT in a tree? Is that even a legitimate statement?

Another serious issue with phylogenetics is that it necessarily assumes that when you describe characters for something, you're describing a unique species (well, unique as in it's a different species from the rest of the species being analyzed). The math WILL give a result; it can't NOT give a result. If you include two members of the same species it'll produce a result. What this means is that phylogeny alone can never determine if organisms are unique species or not--regardless of what methods are used. Any argument that two things must be the same species is necessarily done either before or after the fact.

 

[Kotatsu]

That's depressing. I know that in paleontology there's still a big enough push for morphology that even those who use genetics need to have a basic understanding of the taxa they're examining, but that's as much due to inertia as anything else (for hundreds of years we had nothing BUT morphology to work with, so paleontology focuses on morphology). It's rather frightening that this isn't the case for the squishier fields of biology.

It's all to do with the impression people have of taxonomy as people moving beetles between boxes and getting upset that someone misspells "coeruleirhamphus". Sure, they will have a basic understanding of the taxa they work with -- maybe being able to identify most species to genus level -- but there are so many phylogeneticists who are working in the field mainly because they want to test their various methods or are interested in statistics or something, and don't really care what group of organisms they are working with, as long as the methods apply and they get to tell cool stories about the data.

This is of course even more true of non-phylogeneticists. I think my favorite example of this was when I was writing a chapter on cryptic speciation in oligochaetes for a book on using annelids as model organisms, and we came across a great paper on some leech (I have forgotten the genus...) that was being used as a model organism for evo-devo studies of segmentation. It was a common species in the US and Canada, and therefore it had been selected as the model organism, and too much energy had been put into researching things to change, even when the researchers in various labs across the world started to realise that data from different labs were incompatible. I don't know evo-devo, so I can't say what it was that didn't add up more precisely, but there were plenty of examples where results from a lab in California directly contradicted results in Florida, even when the authors worked together.

So the authors of the paper we looked at gathered leeches from all these labs, as well as from the wild, including a lot of other leeches from the same genus, and made a simple two-gene phylogeny. Of course, the lab leeches were found to belong to (I think) six different species of two different genera, and these could easily be told apart morphologically if you knew the characters. But it was easier, apparently, to just go out and get leeches from your nearest brook and assume that these were the same species, than to approach a taxonomist and have them double-check this.

This is my favorite examples, because it shows that even people who work with pretty advanced stuff like evo-devo still need us beetle-movers...

With genetic data, it can be even worse. Go to GenBank and search for virtually any higher taxon, and you will get about 1/5-1/2 of the results being identified only to genus or family level, or sometimes only labelled "Ecological sample #14561561". In many cases, of course this is because the species are truly unknown, but I would say that in as many cases, this is because the researchers couldn't immediately identify the species to more than genus, couldn't be bothered to check the taxonomic literature, and didn't contact anyone who knew the characters.

These things ca be very frustrating sometimes.

Some traits are simply due to the structural necessities of other traits--Gould had a name for them, but it always eludes me.

Exaptation?

And if you really want to mess with your head, try to figure out how chronospecies fit into this. Bison antiquis essentially turned into modern bison (creatively enough, B. bison) wholesale. How do you represent THAT in a tree? Is that even a legitimate statement?

Thinking about these things is why there are still so many people who believe we should recognise paraphyletic groups... and why there are still people who seem to believe that the phylocode is somehow a good idea. I was a bit dismayed when I recently got a copy of Martyniuk's "Field Guide to Mesozoic Birds and other winged dinosaurs" and saw that in a book from 2012, some people are still advocating the phylocode. I thought that had died away... (great book otherwise, though)

Another serious issue with phylogenetics is that it necessarily assumes that when you describe characters for something, you're describing a unique species (well, unique as in it's a different species from the rest of the species being analyzed). The math WILL give a result; it can't NOT give a result. If you include two members of the same species it'll produce a result. What this means is that phylogeny alone can never determine if organisms are unique species or not--regardless of what methods are used. Any argument that two things must be the same species is necessarily done either before or after the fact.

And this is of course exacerbated somewhat the more closely related the species are believed to be, especially if very few (1-2) individuals of each taxon are included, as this is likely to give too much prominence to evolutionarily insignificant random mutations that just represent individual variation, rather than some actual differences between the taxa that are well established in the population.

 

[Jodie]

Maybe this has been covered before, but in what way is genetic data less subjective than morphological data?

People who do genetic phylogenies will still need to chose the genes they will sequence (1), and they will need to chose which gene trees to publish, or at least which gene trees to put most emphasis on if the different genes show different things. There are thousands of published phylogenies out there where the authors clearly want a certain scenario to be true, and therefore put more emphasis on trees that are concordant with that scenario, and relegate mismatching trees to "Electronic material" or simply do not publish it.

There's also (at least in the past, I haven't done any sequencing for a few years) the issue of reading chromatographs and trying to establish in tricky areas which of two equally high peaks in a certain position is the accurate one, or if both are accurate, and if so what to do with them: prune? use one of those hybrid letters? decide on one letter?

What method do you use to align your data set? What do you do with hypervariable sections? Do you include or exclude the primer regions from the alignment? If you use multiple analysis methods (parsimony, bayesian, likelihood, and so on) what parametres do you use? Do you treat trees from all three analyses equally? What if they don't say the same thing? Which analyses will you put in "Electronic supplements" or just not publish? If you get an unexpected or very unlikely placement of a taxon, do you just cut it out, resequence it (from the same or a different specimen?), or see this as a result in itself? Do you try to ascertain that the specimen is actually the taxon you thought it was, or do you just assume that it is (2)? How do you chose an outgroup? How do you select which taxa should be included in the ingroup? Do you change these two to get the results you want? (3)

These are just some of the long list of reasons why a genetic phylogeny is about as subjective as one based on morphology. What can generally be said is that someone who takes the time to construct a morphological data set and turn that into a phylogeny probably has a more intimate knowledge of the group in question that someone who only see the taxa as small samples in tubes from which they will extract DNA.

When I worked with bird phylogenies as an undergraduate-equivalent, I was given bags with feathers in them and extracted DNA from them. I had no idea whether the identification of the taxa was correct, and the feathers (from warblers, finches, and sparrows, mainly) were too uniform to be able to tell anything useful from studying the feathers. Now that I also do morphology, and am lucky enough to be in a lab that sees the worth of combining morphology and genetics in reconstructing phylogenies, I understand the group I'm working with (feather lice) infinitely better than I did when I worked with birds.

Case in point: a friend of mine was working with the systematics of a minor phylum of animals, on which there are about three living experts. His supervisor didn't know anything about the group, but had still somehow managed to get funding for this PhD project, so they looked up these few experts, and found that only one was in Europe, where my friend was also living. It would make more sense to fly down to Italy from Sweden every now and then, than to fly to (I think) South America and Australia where the only other two experts worked.

So my friend collected a lot of material, sequenced this, and brought it to Italy, where he was going to collaborate with the expert and make the first phylogeny of the group to incorporate all described families. However, when the results came back from the (I think) Bayesian analysis, there were lots of species that came out in the "wrong" family, and the trees made little sense when compared to the scenario of the evolution of this group that the Italian professor had already proposed (presumably based on morphology or on smaller data sets; I don't know). The Italian therefore started deleting taxa from the data set that he thought were placed in the wrong part of the tree,until he got the scenario he wanted. My friend tried to stop him, but the Italian simply pointed out that he was the professor, my friend was the PhD student, this was the professor's lab, and therefore they were going to do things his way. Luckily, my friend had saved all the data.

This story is meant to show one thing: it doesn't matter what data you have, because it's going to be filtered through a human at some point, and then all pretense of absolute objectivity vanishes immediately. There is no actual qualitative difference between the objectivity of genetic characters and morphological characters; there is only a difference in how they are treated.

The statement that genetic data is less subjective than morphological data is a myth, perpetuated mainly by people who have a vested interest in getting their publications into higher-ranking journals or getting more funding.

---
(1) Unless, of course, this is chosen for them. There are only a handful of primer-pairs that have been used for louse phylogenies, for instance, because early on there were only a few that could be made to work, and this has sort of channeled new sequencing into certain gene regions, as people want to compare new data with old data, or incorporate older sequences in new data sets. This is true for most unpopular groups of organisms (i.e. everything except birds and wasps...).
(2) Many phylogeneticists DO NOT KNOW the species they are working with intimately enough to be able to tell closely related species apart. They have no interest in taxonomy, and do not even try to make sure that the name they are using is actually the correct one.
(3) Of course, many of these issues exist with morphological data as well.

I would think it would be less subjective based on how it's used in the medical field in relation to genetic diseases that I'm more familiar with. If they can establish those relationships it seems like it would be easier to do basic identification through DNA analysis.

Do you mind contributing to the Sykes DNA thread here on JREF? The recent shows on Channel 4 have identified some type of new bear in the Himalayas that has mtDNA from an ancient polar bear. Maybe you can figure out how he came to that conclusion, the peer reviewed paper isn't out yet.

 

[Akri]

I would think it would be less subjective based on how it's used in the medical field in relation to genetic diseases that I'm more familiar with. If they can establish those relationships it seems like it would be easier to do basic identification through DNA analysis.

It doesn't matter what it "seems like". What matters is the evidence.

ETA: Are you honestly just going to shrug your shoulders at everything Kotatsu just said, and dismiss it because it "seems to you" that genetic data is less subjective--even though you were just given a 1,029 word explanation on how it's at least as subjective as morphological data?

 

[Kotatsu]

I would think it would be less subjective based on how it's used in the medical field in relation to genetic diseases that I'm more familiar with. If they can establish those relationships it seems like it would be easier to do basic identification through DNA analysis.

Yes, well, then you would be misguided. There is no qualitative difference between morphological and genetic data, in the sense that genetic data is essentially morphological data but at a molecular level. A genetic sequence is nothing but a glorified description of the morphology of a particular piece of that organism's DNA molecules; traditional morphological data is just a description of parts of the organism that can be directly observed (whether unaided or with e.g. a microscope). There is no difference. The difference in what level of subjectivity you are at when you analyse this kind of data, depends entirely on how competently you handle your data set regardless of what kind of data it is made up from.

This is immediately obvious when you realise that very often, nuclear and mitochondrial data do not give you the same phylogeny. I have no numbers for all organisms, but in my experience (birds, bird lice, wasps, bovids, oligochaetes), this is true for at least some branch or support value for about 99% of all genetic data sets. And as soon as there is such a discrepancy between two data sets, it does not really matter what sort of data it is based on, what matters is how you handle this. Do you prefer one result over another? If so, you are being subjective. Do you present all data and present reasoned explanations both for all scenarios suggested by the data, and for the presence of discrepancies? Then you are being at least honest, but pretty much every time you read a phylogenetic paper that has this kind of issue, it is obvious that the authors believe one of the scenarios to be more reasonable than the other, and there subjectivity creeps in again.

As to doing basic identification, you need to do the morphology first anyway, so no, it does not actually help. I can have a thousand whole-genome sequences, but that does not mean anything if I haven't already identified the organisms so that I know what name to put on which sequence. And for all but a minute fraction of the known species (1), identifying organisms means looking at morphology. Once you've done that, and built up a large data base with which to compare, you can identify organisms by sequences, but that is unfortunately still not the case for the vast majority of organisms.

Do you mind contributing to the Sykes DNA thread here on JREF? The recent shows on Channel 4 have identified some type of new bear in the Himalayas that has mtDNA from an ancient polar bear. Maybe you can figure out how he came to that conclusion, the peer reviewed paper isn't out yet.

I don't know what this thread is, and know from experience that I too easily get pulled into discussions here that take up too much of my time, so probably not. Having polar bear mtDNA in a non-polar bear population could be something as simple as incomplete lineage sorting, introgression, or some other well-known phenomenon, but it's probably going to be impossible to tell without seeing the data.

---
(1) Off the top of my head, the only species I can think of that definitely requires DNA to tell it apart from its relatives, and where no morphological character known can be used, is Enchytraeus crypticus. However, even in this case I believe environmental data can be used to tell it apart from its closest relative (I have forgotten which species this is). That does not mean, however, that this is always going to be the case. As far as I know, no one has ever looked at sperm ultrastructure in these worms, so there may be characters there.

 

[Jodie]

What a shame, here it is if you find a minute:

http://www.internationalskeptics.com/forums/showthread.php?t=267046

 

[EHocking]

What a shame, here it is if you find a minute:

http://www.internationalskeptics.com/forums/showthread.php?t=267046

I think that, like the rest of us on that thread, Kotatsu's last point is the most salient,

it's probably going to be impossible to tell without seeing the data
​

Sykes has not produced a paper on this "yet".
All comments are thus mere speculation on hearsay from media sources and soundbites.

 

[Akri]

What a shame, here it is if you find a minute:

http://www.internationalskeptics.com/forums/showthread.php?t=267046

Care to comment on the part of Kotatsu's post that's actually relevant to this thread?

 

[Kotatsu]

What a shame, here it is if you find a minute:

http://www.internationalskeptics.com/forums/showthread.php?t=267046

I have skimmed that thread now, and will retain my previous opinion, quoted by EHocking. it is, in any case, nothing that interests me very much, until there as an actual specimen, collected under controlled conditions, so that the purported new bear species could be described properly. A few hairs are as useful and interesting as "Environmental sample #41661562" to me; it does not say anything, regardless of what it may or may not match.

But please feel free to explain how genetic data is less subjective than morphological data, given the concerns I have outlined in several posts now.

 

[Dinwar]

I would think it would be less subjective based on how it's used in the medical field in relation to genetic diseases that I'm more familiar with.

Well THERE'S your problem!

More seriously, this is a problem. You're not comparing apples to apples, but rather apples to space shuttles. You may know a great deal about genetics as it applies to your field (I seriously doubt it, as you've made some egregious errors in this thread and elsewhere, but I'm willing to accept it ad arguendum) and have assumed that you therefore know this entire topic. The problem is, you don't. You demonstrably can't even identify the other side properly, much less articulate what the other side is saying. Therefore you are comparing--at best--YOUR KNOWLEDGE OF one field with YOUR KNOWLEDGE OF another. The fact that the side you know little to nothing about came out the worse in such a comparison is a foregone conclusion, and says nothing about the field.

Here's the thing: the doctors who do that genetic work know what they're looking for. Those genetic codes have been studied well enough and in such a way that clear field markers have been devised to facilitate identification. This is completely different from basic research in genetic phylogeny, which involves discovering those field markers as one step in many.

I have skimmed that thread now, and will retain my previous opinion, quoted by EHocking. it is, in any case, nothing that interests me very much, until there as an actual specimen, collected under controlled conditions, so that the purported new bear species could be described properly. A few hairs are as useful and interesting as "Environmental sample #41661562" to me; it does not say anything, regardless of what it may or may not match.

I was reminded today of just how easily contamination can creep into research. Even something as simple as the sample being exposed to air can contaminate it. If all you have is a few hairs, you'd better make DAMN sure those hairs came from what you think they came from! And after experience with dogs and cats, I can attest to the ability of hair to get in places you'd think were prefectly safe from it.

So Step 1 for these researchers is--as is the case for all of us--to demonstrate that what they're examining is what they think it is. If they got some polar bear hair in with the rest, the answer may be as simple as "They screwed up."

(1) Off the top of my head, the only species I can think of that definitely requires DNA to tell it apart from its relatives, and where no morphological character known can be used, is Enchytraeus crypticus.

I thought a number of bacteria/Archea species were identifiable only via DNA. We're generally talking animals in this thread, but other kingdoms and domains operate differently, and I can't imagine there being too much morphological difference between microscopic species (we didn't know Archea was a thing until genetic studies, after all!). I could be completely off base, though; the microscopic world is one I only dabble in, since I prefer dealing with predatory megafauna.

 

[Kotatsu]

I thought a number of bacteria/Archea species were identifiable only via DNA. We're generally talking animals in this thread, but other kingdoms and domains operate differently, and I can't imagine there being too much morphological difference between microscopic species (we didn't know Archea was a thing until genetic studies, after all!). I could be completely off base, though; the microscopic world is one I only dabble in, since I prefer dealing with predatory megafauna.

Ah, well you know me, I readily forget that non-animals even exist... There are of course lots of unicellular organisms, as well as probably plants and fungi that also require DNA to identify them. I'm just too much of a zoologist to remember these less interesting kingdoms...

 

[Kotatsu]

I was reminded today of just how easily contamination can creep into research. Even something as simple as the sample being exposed to air can contaminate it. If all you have is a few hairs, you'd better make DAMN sure those hairs came from what you think they came from! And after experience with dogs and cats, I can attest to the ability of hair to get in places you'd think were prefectly safe from it.

So Step 1 for these researchers is--as is the case for all of us--to demonstrate that what they're examining is what they think it is. If they got some polar bear hair in with the rest, the answer may be as simple as "They screwed up."

A note on this, as well.

When I was doing a lot of DNA sequencing every day as an undergraduate-equivalent (1), we had a problem one day that all the sequences I got back from Korea (where we sent the purified post-PCR products to get the sequences more cheaply) were suddenly wasps, instead of oligochaetes. Now, this didn't seem like such a big deal, as I was working both for a profesupr who specialized in oligochaetes and a lecturer who did wasps on the side. This could thus have been a simple mix-up between samples.

However, when we started looking in our lab log books to see if we could trace the problem, two things were immediately apparent:
- When I started sequencing wasps, I had already sent these samples to Korea, so I couldn't possibly have mixed them up;
- The wasps were not the Swedish wasps that the lecturer was working on, but some Neotropical group (or maybe Australian, it's been seven years and I can't remember), and there was no one in the whole house who worked with Neotropical animals, and no one else who worked with wasps.

We considered the possibility that, since I had only got this result for one gene (COI, I think), but not for the other genes I had sequenced for the same specimens, this may be some weird form of extreme convergence, so that by chance, the COI sequence of this worm species was more similar to wasp DNA than to other worm DNA, when compared on GenBank. A ludicrous proposal, of course, but one that could easily be checked by simply re-sequencing the same gene for the same specimens and see if we got the same wasp-gene results. Of course, we didn't get the same result, and the new sequences were what we would expect them to be, and places the specimens in the same place in the phylogeny as the other genes did. My professor then choose not to pursue this in any way.

Still, the point is that this is the proper thing to do. If you get very strange results, double-check, and if you still get the same strange results, you go and try to get more samples from the same species on the same locality, study the whole morphology, make sure that there is no possibility of a mix-up or a misidentification, and then, when you are entirely satisfied, you can go public with this mysterious data. Otherwise, you may end up as an older PhD student I know of.

There is a creature called Xenoturbella which has been very hard to place in the tree of life, mainly because it has a very reduced body plan, so there is very little to compare with other organisms. The Wikipedia entry on this genus hints at how it was once thought to be a mollusc, but it doesn't give the details of why it was believed to be a mollusc. Here is the story as I heard it (and as I remember it, so it may not be entirely accurate) from my old professor, who was in the lab at the time when the Nature article referred to in the Wiki article was published.

There was at that time, at the university where my old professor used to work, a professor with two PhD students. One was working on morphology of some marine invertebrates, and the other was working on the higher-order genetic phylogeny of the same groups. The latter had been sequencing a lot of different organisms (which was more difficult back in the mid-90s than it is now), including Xenoturbella, and had got some interesting results. Xenoturbella was a mollusc!

Excitedly, he went to the professor, and reported these wonderful news. DNA had finally solved the puzzle, and they were the ones who had discovered it! Fame and glory in the invertebrate systematics world awaited them, and they were going to try to get this published in as good a journal as possible.

There was one problem, though, and that was the other PhD student. He had overheard this whole story, and remembered that he had some Xenoturbella samples of his own. So he quickly dissected some worms, put them on slides, found mollusc-type eggs in some of his Xenoturbella and, without telling his professor, wrote up a paper to send to Nature. It was accepted, of course, as this was incredibly interesting news, and once it was accepted, the student went to the professor with the manuscript, proud to be able to show that he had got one of his first papers into Nature!

The professor was of course furious that he had been scooped like that, and I don't know what happened after this, but in that edition of Nature, the two papers occur side by side, with the molecular paper preceding the morphological paper. Notably, the morphological paper has only one author, while the molecular paper has both the professor and the other PhD student on it. I'm guessing Nature thought it was twice as good to have both genetic and morphological data for the same conclusion, regardless of how the results had come about.

If the story had ended there, there would have been no point in telling it, and as we're talking about contaminations and the need to check strange results again, anyone who read this has probably already figured out how this continues. Of course, it was discovered afterwards that Xenoturbella eats molluscs, and that the eggs that had been found inside it were actually molluscan eggs that had just not been digested yet, and the DNA was also from ingested material. It took 6 years to figure this out, however, and Xenoturbella is today placed in its own phylum (Xenacoelomorpha) together with the acoelomorph flatworms.

This story shows the importance of double-checking. If they had sequenced another worm, maybe they wouldn't have got the same contaminated sequence, and this would hopefully have caused them to do it again to settle the matter. And this would not have lead the other PhD student to go and actively look for something to connect the Xenoturbella to molluscs in his morphological samples.

For reasons such as these two (wasps and Xenoturbella; and there are of course many more), I remain very skeptical of extraordinary claims based on extremely little data. Like I said, when they have a whole specimen of this purported new bear/ancient polar bear/whatever, then I will be interested, but until then, there are just too many things that can go wrong...

---
(1) It works differently in my home country. By the time I did this, I already had a Masters, but was working in a lab doing menial tasks for more money than graduate students get in my present lab in Salt Lake City...

 

[Dinwar]

I have a vague recollection that parasites can transmit genes to their hosts--I believe they found leach genes in humans, for example. Is that true? I know it's not terribly common (it's one, maybe two, genes, in a few thousand years of people being bitten, as I recall), but it's always possible that the researcher selected the exact worst gene to look at. Retroviruses are another potential vector. If so, it certainly would emphasize the necessity to at least use multiple genes in a genetic study, and would definitely demonstrate that one needs to be VERY careful when selecting genes to analyze!